SMTL ID : 11bg.2 (1 other biounit)

A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BOVINE SEMINAL RIBONUCLEASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: Q.11, H.12 Chain B: K.41, H.119, F.120 Ligands: U2G.12 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: K.39, C.40, K.41, P.42 Ligands: U2G.8 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: S.18, P.19, S.20, S.21 Chain B: Q.101 Chain C: S.21, S.22 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: K.39 Chain B: K.7, Q.11 Ligands: U2G.8 Ligand excluded by PLIP SO4.5: 7 residues within 4Å: Chain A: K.41, H.119, F.120 Chain B: Q.11, H.12 Ligands: U2G.6, U2G.8 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: K.7, Q.11 Chain B: K.39 Ligand excluded by PLIP SO4.10: 9 residues within 4Å: Chain B: S.20, S.21, S.22, S.23 Chain D: S.20, S.21, S.22, S.23 Ligands: SO4.22 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: K.39, K.41, P.42 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain C: Q.11, H.12 Chain D: K.41, H.119, F.120 Ligands: U2G.24 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain C: K.39, C.40, K.41, P.42 Ligands: U2G.20 Ligand excluded by PLIP SO4.15: 7 residues within 4Å: Chain A: S.21, S.22 Chain C: S.18, P.19, S.20, S.21 Chain D: Q.101 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: K.39 Chain D: K.7, Q.11 Ligands: U2G.20 Ligand excluded by PLIP SO4.17: 7 residues within 4Å: Chain C: K.41, H.119, F.120 Chain D: Q.11, H.12 Ligands: U2G.18, U2G.20 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: K.7, Q.11 Chain D: K.39 Ligand excluded by PLIP SO4.22: 9 residues within 4Å: Chain B: S.20, S.21, S.22, S.23 Chain D: S.20, S.21, S.22, S.23 Ligands: SO4.10 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain D: K.39, K.41, P.42 Ligand excluded by PLIP

8 x U2G: URIDYLYL-2'-5'-PHOSPHO-GUANOSINE(Non-covalent)

U2G.6: 15 residues within 4Å: Chain A: V.43, N.44, T.45, K.66, R.85, V.102, K.104, H.119, F.120, D.121, A.122, S.123 Chain B: H.12 Ligands: SO4.5, U2G.8 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.45, A:K.66, A:R.85, A:S.123, A:S.123 Water bridges: A:T.45, A:D.83 Salt bridges: A:K.104 U2G.7: 8 residues within 4Å: Chain A: D.14, N.24, N.27, L.28, N.94, C.95 Chain B: C.32, R.33 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.14, A:D.14, A:N.24, A:N.24, A:N.27, A:C.95, B:R.33 Water bridges: B:R.33 U2G.8: 8 residues within 4Å: Chain A: K.39, K.41, P.42 Chain B: Q.11 Ligands: SO4.2, SO4.4, SO4.5, U2G.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.39, A:K.39, B:Q.11 Water bridges: A:V.43 U2G.12: 12 residues within 4Å: Chain A: H.12 Chain B: V.43, N.44, T.45, N.67, D.83, R.85, F.120, D.121, A.122, S.123 Ligands: SO4.1 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.45, B:N.67, B:N.67, B:D.83, B:R.85, B:S.123 Water bridges: B:T.45, B:S.123, B:S.123 Salt bridges: B:R.85 U2G.18: 15 residues within 4Å: Chain C: V.43, N.44, T.45, K.66, R.85, V.102, K.104, H.119, F.120, D.121, A.122, S.123 Chain D: H.12 Ligands: SO4.17, U2G.20 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.45, C:T.45, C:K.66, C:R.85, C:S.123, C:S.123 Salt bridges: C:K.104 U2G.19: 8 residues within 4Å: Chain C: D.14, N.24, N.27, L.28, N.94, C.95 Chain D: C.32, R.33 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.14, C:N.24, C:N.24, C:N.27, C:C.95, D:R.33 Water bridges: D:R.33 U2G.20: 8 residues within 4Å: Chain C: K.39, K.41, P.42 Chain D: Q.11 Ligands: SO4.14, SO4.16, SO4.17, U2G.18 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.39, C:K.39, D:Q.11 Water bridges: C:V.43 U2G.24: 12 residues within 4Å: Chain C: H.12 Chain D: V.43, N.44, T.45, N.67, D.83, R.85, F.120, D.121, A.122, S.123 Ligands: SO4.13 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.45, D:T.45, D:N.67, D:N.67, D:R.85, D:S.123 Water bridges: D:S.123, D:S.123, D:S.123 Salt bridges: D:R.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vitagliano, L. et al., A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease. J.Mol.Biol. (1999)

Release Date

1999-11-05

Peptides

PROTEIN (BOVINE SEMINAL RIBONUCLEASE): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PROTEIN (BOVINE SEMINAL RIBONUCLEASE)

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